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- PDB-4p52: Crystal structure of homoserine kinase from Cytophaga hutchinsoni... -

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Basic information

Entry
Database: PDB / ID: 4p52
TitleCrystal structure of homoserine kinase from Cytophaga hutchinsonii ATCC 33406, NYSGRC Target 032717.
ComponentsHomoserine kinase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


homoserine kinase / homoserine kinase activity / threonine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Homoserine kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...Homoserine kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Homoserine kinase / Homoserine kinase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of homoserine kinase from Cytophaga hutchinsonii ATCC 33406, NYSGRC Target 032717.
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Structure summary
Revision 1.2Sep 27, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_polymer_linkage / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homoserine kinase


Theoretical massNumber of molelcules
Total (without water)35,3991
Polymers35,3991
Non-polymers00
Water2,198122
1
A: Homoserine kinase

A: Homoserine kinase


Theoretical massNumber of molelcules
Total (without water)70,7982
Polymers70,7982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
Buried area2780 Å2
ΔGint-24 kcal/mol
Surface area25780 Å2
MethodPISA
2
A: Homoserine kinase

A: Homoserine kinase


Theoretical massNumber of molelcules
Total (without water)70,7982
Polymers70,7982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area2730 Å2
ΔGint-18 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.608, 101.608, 195.982
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

21A-446-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Homoserine kinase / / HSK


Mass: 35399.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / NCIMB 9469 / Gene: thrB, CHU_0074 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: Q11YZ8, UniProt: A0A6N4SM98*PLUS, homoserine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.2M Na2HPO4/KH2PO4, pH 6.2, 2.5M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 34842 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.141 / Χ2: 1.735 / Net I/av σ(I): 17.474 / Net I/σ(I): 7.4 / Num. measured all: 219070
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.645.70.76917301.208100
2.64-2.695.70.67317401.25199.7
2.69-2.745.70.55117501.2299.9
2.74-2.85.80.53417471.241100
2.8-2.865.90.48617171.22499.7
2.86-2.9360.43917481.271100
2.93-360.36417341.28899.9
3-3.086.10.30317561.32899.9
3.08-3.176.20.24217551.35499.9
3.17-3.286.30.19917351.443100
3.28-3.396.40.16517531.523100
3.39-3.536.50.1417261.616100
3.53-3.696.50.12517291.664100
3.69-3.886.50.12117542.063100
3.88-4.136.50.10917292.452100
4.13-4.456.50.117542.901100
4.45-4.896.60.08917622.979100
4.89-5.670.08617372.4799.9
5.6-7.057.10.07617451.693100
7.05-506.90.04517411.88898.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SHELXphasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
PHENIXmodel building
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.974 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.209 960 5 %RANDOM
Rwork0.1723 18107 --
obs0.1741 19067 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.18 Å2 / Biso mean: 39.363 Å2 / Biso min: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.58 Å20 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 2.6→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 0 122 2451
Biso mean---37.28 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192365
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9923205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.88625.68288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23615383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.206158
X-RAY DIFFRACTIONr_chiral_restr0.0980.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211744
X-RAY DIFFRACTIONr_mcbond_it1.976.1661258
X-RAY DIFFRACTIONr_mcangle_it3.33898.9211569
X-RAY DIFFRACTIONr_scbond_it4.2857.4341107
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 73 -
Rwork0.237 1281 -
all-1354 -
obs--99.71 %
Refinement TLS params.Method: refined / Origin x: 60.9524 Å / Origin y: 29.8655 Å / Origin z: 17.2392 Å
111213212223313233
T0.0302 Å2-0.0156 Å20.0043 Å2-0.0662 Å2-0.0177 Å2--0.0309 Å2
L0.5616 °20.2862 °2-0.2517 °2-1.1477 °2-0.6302 °2--1.5599 °2
S-0.0053 Å °-0.0231 Å °-0.0739 Å °-0.0533 Å °-0.042 Å °-0.0781 Å °0.1919 Å °0.0186 Å °0.0473 Å °

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